CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment

Ping Wang, Mingyan Lin, Erika Pedrosa, Anastasia Hrabovsky, Zheng Zhang, Wenjun Guo, Herbert M. Lachman, Deyou Zheng

Research output: Contribution to journalArticle

55 Citations (Scopus)

Abstract

Background: Disruptive mutation in the CHD8 gene is one of the top genetic risk factors in autism spectrum disorders (ASDs). Previous analyses of genome-wide CHD8 occupancy and reduced expression of CHD8 by shRNA knockdown in committed neural cells showed that CHD8 regulates multiple cell processes critical for neural functions, and its targets are enriched with ASD-associated genes. Methods: To further understand the molecular links between CHD8 functions and ASD, we have applied the CRISPR/Cas9 technology to knockout one copy of CHD8 in induced pluripotent stem cells (iPSCs) to better mimic the loss-of-function status that would exist in the developing human embryo prior to neuronal differentiation. We then carried out transcriptomic and bioinformatic analyses of neural progenitors and neurons derived from the CHD8 mutant iPSCs. Results: Transcriptome profiling revealed that CHD8 hemizygosity (CHD8 +/-) affected the expression of several thousands of genes in neural progenitors and early differentiating neurons. The differentially expressed genes were enriched for functions of neural development, β-catenin/Wnt signaling, extracellular matrix, and skeletal system development. They also exhibited significant overlap with genes previously associated with autism and schizophrenia, as well as the downstream transcriptional targets of multiple genes implicated in autism. Providing important insight into how CHD8 mutations might give rise to macrocephaly, we found that seven of the twelve genes associated with human brain volume or head size by genome-wide association studies (e.g., HGMA2) were dysregulated in CHD8 +/- neural progenitors or neurons. Conclusions: We have established a renewable source of CHD8 +/- iPSC lines that would be valuable for investigating the molecular and cellular functions of CHD8. Transcriptomic profiling showed that CHD8 regulates multiple genes implicated in ASD pathogenesis and genes associated with brain volume.

Original languageEnglish (US)
Article number48
JournalMolecular Autism
Volume6
Issue number1
DOIs
StatePublished - Dec 1 2015

Fingerprint

Clustered Regularly Interspaced Short Palindromic Repeats
Gene Knockout Techniques
Gene Regulatory Networks
Autistic Disorder
Genes
Induced Pluripotent Stem Cells
Neurons
Megalencephaly
Catenins
Mutation
Genome-Wide Association Study
Brain
Gene Expression Profiling
Computational Biology
Small Interfering RNA
Extracellular Matrix
Schizophrenia
Embryonic Structures
Head
Genome

Keywords

  • ASD
  • Autism
  • CHD8
  • CRISPR/Cas9
  • Induced pluripotent stem cells
  • iPSC
  • Macrocephaly
  • Neurodevelopment
  • RNA-seq
  • Schizophrenia

ASJC Scopus subject areas

  • Psychiatry and Mental health
  • Developmental Neuroscience
  • Developmental Biology
  • Molecular Biology

Cite this

CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment. / Wang, Ping; Lin, Mingyan; Pedrosa, Erika; Hrabovsky, Anastasia; Zhang, Zheng; Guo, Wenjun; Lachman, Herbert M.; Zheng, Deyou.

In: Molecular Autism, Vol. 6, No. 1, 48, 01.12.2015.

Research output: Contribution to journalArticle

@article{44d78dc3f6ad422d822b2aaee73395c4,
title = "CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment",
abstract = "Background: Disruptive mutation in the CHD8 gene is one of the top genetic risk factors in autism spectrum disorders (ASDs). Previous analyses of genome-wide CHD8 occupancy and reduced expression of CHD8 by shRNA knockdown in committed neural cells showed that CHD8 regulates multiple cell processes critical for neural functions, and its targets are enriched with ASD-associated genes. Methods: To further understand the molecular links between CHD8 functions and ASD, we have applied the CRISPR/Cas9 technology to knockout one copy of CHD8 in induced pluripotent stem cells (iPSCs) to better mimic the loss-of-function status that would exist in the developing human embryo prior to neuronal differentiation. We then carried out transcriptomic and bioinformatic analyses of neural progenitors and neurons derived from the CHD8 mutant iPSCs. Results: Transcriptome profiling revealed that CHD8 hemizygosity (CHD8 +/-) affected the expression of several thousands of genes in neural progenitors and early differentiating neurons. The differentially expressed genes were enriched for functions of neural development, β-catenin/Wnt signaling, extracellular matrix, and skeletal system development. They also exhibited significant overlap with genes previously associated with autism and schizophrenia, as well as the downstream transcriptional targets of multiple genes implicated in autism. Providing important insight into how CHD8 mutations might give rise to macrocephaly, we found that seven of the twelve genes associated with human brain volume or head size by genome-wide association studies (e.g., HGMA2) were dysregulated in CHD8 +/- neural progenitors or neurons. Conclusions: We have established a renewable source of CHD8 +/- iPSC lines that would be valuable for investigating the molecular and cellular functions of CHD8. Transcriptomic profiling showed that CHD8 regulates multiple genes implicated in ASD pathogenesis and genes associated with brain volume.",
keywords = "ASD, Autism, CHD8, CRISPR/Cas9, Induced pluripotent stem cells, iPSC, Macrocephaly, Neurodevelopment, RNA-seq, Schizophrenia",
author = "Ping Wang and Mingyan Lin and Erika Pedrosa and Anastasia Hrabovsky and Zheng Zhang and Wenjun Guo and Lachman, {Herbert M.} and Deyou Zheng",
year = "2015",
month = "12",
day = "1",
doi = "10.1186/s13229-015-0048-6",
language = "English (US)",
volume = "6",
journal = "Molecular Autism",
issn = "2040-2392",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment

AU - Wang, Ping

AU - Lin, Mingyan

AU - Pedrosa, Erika

AU - Hrabovsky, Anastasia

AU - Zhang, Zheng

AU - Guo, Wenjun

AU - Lachman, Herbert M.

AU - Zheng, Deyou

PY - 2015/12/1

Y1 - 2015/12/1

N2 - Background: Disruptive mutation in the CHD8 gene is one of the top genetic risk factors in autism spectrum disorders (ASDs). Previous analyses of genome-wide CHD8 occupancy and reduced expression of CHD8 by shRNA knockdown in committed neural cells showed that CHD8 regulates multiple cell processes critical for neural functions, and its targets are enriched with ASD-associated genes. Methods: To further understand the molecular links between CHD8 functions and ASD, we have applied the CRISPR/Cas9 technology to knockout one copy of CHD8 in induced pluripotent stem cells (iPSCs) to better mimic the loss-of-function status that would exist in the developing human embryo prior to neuronal differentiation. We then carried out transcriptomic and bioinformatic analyses of neural progenitors and neurons derived from the CHD8 mutant iPSCs. Results: Transcriptome profiling revealed that CHD8 hemizygosity (CHD8 +/-) affected the expression of several thousands of genes in neural progenitors and early differentiating neurons. The differentially expressed genes were enriched for functions of neural development, β-catenin/Wnt signaling, extracellular matrix, and skeletal system development. They also exhibited significant overlap with genes previously associated with autism and schizophrenia, as well as the downstream transcriptional targets of multiple genes implicated in autism. Providing important insight into how CHD8 mutations might give rise to macrocephaly, we found that seven of the twelve genes associated with human brain volume or head size by genome-wide association studies (e.g., HGMA2) were dysregulated in CHD8 +/- neural progenitors or neurons. Conclusions: We have established a renewable source of CHD8 +/- iPSC lines that would be valuable for investigating the molecular and cellular functions of CHD8. Transcriptomic profiling showed that CHD8 regulates multiple genes implicated in ASD pathogenesis and genes associated with brain volume.

AB - Background: Disruptive mutation in the CHD8 gene is one of the top genetic risk factors in autism spectrum disorders (ASDs). Previous analyses of genome-wide CHD8 occupancy and reduced expression of CHD8 by shRNA knockdown in committed neural cells showed that CHD8 regulates multiple cell processes critical for neural functions, and its targets are enriched with ASD-associated genes. Methods: To further understand the molecular links between CHD8 functions and ASD, we have applied the CRISPR/Cas9 technology to knockout one copy of CHD8 in induced pluripotent stem cells (iPSCs) to better mimic the loss-of-function status that would exist in the developing human embryo prior to neuronal differentiation. We then carried out transcriptomic and bioinformatic analyses of neural progenitors and neurons derived from the CHD8 mutant iPSCs. Results: Transcriptome profiling revealed that CHD8 hemizygosity (CHD8 +/-) affected the expression of several thousands of genes in neural progenitors and early differentiating neurons. The differentially expressed genes were enriched for functions of neural development, β-catenin/Wnt signaling, extracellular matrix, and skeletal system development. They also exhibited significant overlap with genes previously associated with autism and schizophrenia, as well as the downstream transcriptional targets of multiple genes implicated in autism. Providing important insight into how CHD8 mutations might give rise to macrocephaly, we found that seven of the twelve genes associated with human brain volume or head size by genome-wide association studies (e.g., HGMA2) were dysregulated in CHD8 +/- neural progenitors or neurons. Conclusions: We have established a renewable source of CHD8 +/- iPSC lines that would be valuable for investigating the molecular and cellular functions of CHD8. Transcriptomic profiling showed that CHD8 regulates multiple genes implicated in ASD pathogenesis and genes associated with brain volume.

KW - ASD

KW - Autism

KW - CHD8

KW - CRISPR/Cas9

KW - Induced pluripotent stem cells

KW - iPSC

KW - Macrocephaly

KW - Neurodevelopment

KW - RNA-seq

KW - Schizophrenia

UR - http://www.scopus.com/inward/record.url?scp=84944382599&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84944382599&partnerID=8YFLogxK

U2 - 10.1186/s13229-015-0048-6

DO - 10.1186/s13229-015-0048-6

M3 - Article

AN - SCOPUS:84944382599

VL - 6

JO - Molecular Autism

JF - Molecular Autism

SN - 2040-2392

IS - 1

M1 - 48

ER -